LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 2.8700001 2.8700001 2.8700001 Created orthogonal box = (0.0000000 -33.961169 0.0000000) to (41.590252 33.961169 7.0300358) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7531717 4.3660670 4.6866905 Created 844 atoms using lattice units in orthogonal box = (0.0000000 -33.961169 0.0000000) to (41.590252 33.961169 7.0300358) create_atoms CPU = 0.003 seconds 844 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7531717 4.3660670 4.6866905 Created 844 atoms using lattice units in orthogonal box = (0.0000000 -33.961169 0.0000000) to (41.590252 33.961169 7.0300358) create_atoms CPU = 0.002 seconds 844 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 14 23 3 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 1668 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_024705128470_000#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.106 | 5.106 | 5.106 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6927.8126 0 -6927.8126 27242.677 68 0 -7088.8085 0 -7088.8085 2927.7705 Loop time of 1.3723 on 1 procs for 68 steps with 1668 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6927.81257806317 -7088.8020433074 -7088.80853851541 Force two-norm initial, final = 116.07112 0.29214339 Force max component initial, final = 16.864864 0.044344770 Final line search alpha, max atom move = 1.0000000 0.044344770 Iterations, force evaluations = 68 125 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3046 | 1.3046 | 1.3046 | 0.0 | 95.07 Neigh | 0.041035 | 0.041035 | 0.041035 | 0.0 | 2.99 Comm | 0.011268 | 0.011268 | 0.011268 | 0.0 | 0.82 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01539 | | | 1.12 Nlocal: 1668.00 ave 1668 max 1668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5539.00 ave 5539 max 5539 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 110182.0 ave 110182 max 110182 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110182 Ave neighs/atom = 66.056355 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.110 | 5.110 | 5.110 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -7088.8085 0 -7088.8085 2927.7705 19859.198 70 0 -7088.832 0 -7088.832 932.63803 19883.328 Loop time of 0.0524721 on 1 procs for 2 steps with 1668 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7088.80853851541 -7088.83101345551 -7088.8319518146 Force two-norm initial, final = 45.290174 0.29809909 Force max component initial, final = 41.790805 0.043608109 Final line search alpha, max atom move = 0.00016111187 7.0257838e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.049981 | 0.049981 | 0.049981 | 0.0 | 95.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040361 | 0.00040361 | 0.00040361 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002088 | | | 3.98 Nlocal: 1668.00 ave 1668 max 1668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5501.00 ave 5501 max 5501 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 109994.0 ave 109994 max 109994 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109994 Ave neighs/atom = 65.943645 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.248 | 5.248 | 5.248 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7088.832 0 -7088.832 932.63803 Loop time of 2.852e-06 on 1 procs for 0 steps with 1668 atoms 140.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.852e-06 | | |100.00 Nlocal: 1668.00 ave 1668 max 1668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5491.00 ave 5491 max 5491 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 109894.0 ave 109894 max 109894 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109894 Ave neighs/atom = 65.883693 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.248 | 5.248 | 5.248 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -7088.832 -7088.832 41.63415 67.922338 7.0311562 932.63803 932.63803 -0.39649577 2798.3377 -0.027114145 2.2828966 1654.2894 Loop time of 3.344e-06 on 1 procs for 0 steps with 1668 atoms 179.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 3.344e-06 | | |100.00 Nlocal: 1668.00 ave 1668 max 1668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5491.00 ave 5491 max 5491 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54947.0 ave 54947 max 54947 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 109894.0 ave 109894 max 109894 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109894 Ave neighs/atom = 65.883693 Neighbor list builds = 0 Dangerous builds = 0 1668 -7088.8317850146 eV 2.28289660132918 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01